Dr Schmitz joined James Cook University in July 2021. He is an Associate Professor in Bioinformatics at the Department of Molecular & Cell Biology (CPHMVS) and an NHMRC Emerging Leadership Fellow (2021-2025).

Ulf completed his PhD at the University of Rostock (Germany). In 2015, he joined the Centenary Institute in Sydney as a post-doctoral Research Officer in the Gene and Stem Cell Therapy Program. He later established the Computational Biomedicine Lab at the Centenary. He also holds an appointment as Conjoint Senior Lecturer at the University of Sydney (Faculty of Medicine & Health). 

Ulf is a computational biologist with training in bioinformatics and systems biology and more than 12 years of experience in analysing post-transcriptional gene regulation. His research interests focus on computational RNA biology and Systems Medicine. Ulf and his team develop integrative workflows combining various computational disciplines with experimentation to address questions around non-coding RNAs, post-transcriptional gene regulation, and cancer biology. He has published >50 research articles, 10 book chapters, and 4 books on this topic. 

                          

 

Available HDR Student Projects

Portable long-read sequencing to diagnose Chronic Kidney Disease

Determining cellular gene isoform abundance from long-read RNA sequencing data

Mirtron synthesis and expression in leukemia

Alternative splicing-based subtyping of 5k leukaemia and lymphoma samples

Single-cell multi-omics data analysis to elucidate gene isoform regulation in Acute Myeloid Leukemia

Developing a web-tool for animal sequencing data analysis

 

Computational Biomedicine Lab

In the Computational Biomedicine Lab at James Cook University and the Centenary Institute (University of Sydney) computational biologists work hand-in-hand with molecular biologists integrating in silico, in vitro and in vivo approaches in advanced interdisciplinary research. We develop integrative systems medicine workflows along with tools and databases to identify and study interactions between RNAs and other molecules, functional mechanisms of gene regulation, cell signalling pathways and gene regulatory networks.

Our goal is to achieve a deeper understanding of processes involved in disease emergence and progression, with a focus on cancer biology, and possible avenues for therapeutic interventions and optimised treatment schedules. Most projects involve the analysis of experimental high-throughput data (incl. (sc)RNA-seq, NanoString, DNA Methyl-Seq, ChIP-Seq, CLIP-seq, and more). Moreover, we use various mathematical formalisms to model the effects of environmental stimuli or pathogenic events on molecular interaction networks and signalling pathways. Using machine learning and computer simulation approaches, we predict disease progression and outcome as well as the effect of therapeutic agents on cellular survival and resistance mechanisms. 

Current Research Projects

Alternative splicing and the epigenome in Chronic Myeloid Leukaemia

In this project, we are investigating gene regulatory processes in leukaemia. The third biggest cause of cancer death in all Australians is blood cancers (leukaemia), which are diagnosed 35 times each day. Using a multi-omics approach, we examine alternative splicing and epigenetic changes in blood samples from chronic myeloid leukaemia (CML) patients before and after treatment with tyrosine kinase inhibitors. Find out more: Schmitz et al, Cancers 2020

 

Cooperating microRNAs for cancer therapy

In this project, we use a systems medicine approach to find new avenues for overcoming chemotherapy resistance in aggressive tumour cells. Our results suggest that pairs of cooperating microRNAs could be used as potential RNA therapeutics to reduce E2F1-related chemoresistance. Find out more: Lai X, Gupta SK, Schmitz U et al, Theranostics 2018

 

 

Intron retention regulation in haematopoietic cells

There is growing evidence that alternative splicing, including intron retention (IR), is regulated on at least two levels: locally, through a network of interacting trans-acting splicing regulators with cis-acting regulatory elements, and globally, through the chromatin structure. In this project, we explore a global regulation of IR in haematopoietic cells – we use statistical analysis to better understand IR regulation using information derived from the epigenetic factors that govern chromatin organisation, namely nucleosome assembly, DNA methylation, and histone modifications. The main challenge here is to integrate multiple layers of ‘-omics’ into a single computational model which produces biologically interpretable results. Find out more: Petrova et al, bioRxiv 2021

 

 

Cross-talk between post-transcriptional gene regulation mechanisms

Combining computational predictions and in vitro assays, we elucidate the cross-talk between post-transcriptional gene regulation mechanisms. More specifically, we focus on interactions between microRNA molecules and intron-retaining mRNA transcripts and try to identify networks of interconnected gene regulation. Using a systems biology approach we will model competitive post-transcriptional gene regulation through iterative cycles of time-course experiments and model simulations.

 

Portable long-read sequencing to diagnose Chronic Kidney Disease

 

MicroRNAs as Cancer Biomarkers

Teaching

• BC3202: Special Topics in Biochemistry and Molecular Biology (Level 3; TSV)
• BC3203: Bioinformatics (Level 3; TSV)
• BC5203: Advanced Bioinformatics (Level 5; TSV)

Interests

Professional

• Mentoring Early Career Researchers

Research

• RNA Biology
• Cancer Biology
• Bioinformatics
• Systems Biology

Experience

• 2021 to present - A/Prof, James Cook University (Townsville/Australia)
• 2018 to present - Associate Faculty, Centenary Institute (Sydney/Australia)
• 2015 to present - Conjoint Senior Lecturer, University of Sydney (Australia)
• 2018 to 2021 - Senior Research Officer, Centenary Institute (Sydney/Australia)
• 2018 to 2021 - Lab Head, Centenary Institute (Sydney/Australia)
• 2015 to 2017 - Research Officer, Centenary Institute (Sydney/Australia)
• 2003 to 2015 - Systems Engineer, University of Rostock (Germany)

Research Disciplines

• Oncology and carcinogenesis (3211)
• Bioinformatics and computational biology (3102)
• Genetics (3105)

Socio-Economic Objectives

• Expanding knowledge (2801)

Awards

• 2020 - Travel Award - The CASS Foundation
• 2020 - Centenary Recognition Award for Contribution to Centenary Life
• 2016 - Cure the Future Award of Scientific Excellence, Cure the Future Foundation
• 2016 - Joachim-Jungius Award for best PhD thesis at the University of Rostock, Germany

Fellowships

• 2021 to 2025 - NHMRC Investigator (EL1)
• 2018 to 2020 - Cancer Institute NSW Early Career Fellowship
• 2018 to 2019 - Australia-India Strategic Research Fund (AISRF) Early and Mid-Career Fellowship, Australian Academy of Science
• 2017 to 2019 - NHMRC Peter Doherty Fellowship for Early Career Researchers

Other

• 2017 - Honorary Adjunct Professorship at Chhattisgarh Swami Vivekanand Technical University (CSVTU), Bhilai, India
• 2016 - Conjoint Senior Lecturer, Sydney Medical School, University of Sydney

These are the most recent publications associated with this author. To see a detailed profile of all publications stored at JCU, visit ResearchOnline@JCU. Hover over Altmetrics badges to see social impact.

Journal Articles

• Dorney R, Dhungel B, Rasko J, Hebbard L and Schmitz U (in press) Recent Advances in Cancer Fusion Transcript Detection. Briefings in Bioinformatics,
• Karimi M, Karimi A, Abolmaali S, Mehdi S and Schmitz U (2022) Prospects and challenges of cancer systems medicine: from genes to disease networks. Briefings in Bioinformatics, 23 (1).
• Petrova V, Song R, DEEP Consortium , Nordström K, Walter J, Wong J, Armstrong N, Rasko J and Schmitz U (in press) Increased chromatin accessibility facilitates intron retention in specific cell differentiation states. Nucleic Acids Research,
• Shah J, Milevskiy M, Petrova V, Au A, Wong J, Visvader J, Schmitz U and Rasko J (2022) Towards resolution of the intron retention paradox in breast cancer. Breast Cancer Research, 24.
• Wong J and Schmitz U (2022) Intron retention: importance, challenges, and opportunities. Trends in Genetics, 38 (8). pp. 789-792
• Alharbi A, Schmitz U, Bailey C and Rasko J (2021) CTCF as a regulator of alternative splicing: new tricks for an old player. Nucleic Acids Research, 49 (14). pp. 7825-7838
• Bailey C, Gupta S, Metierre C, Amarasekera P, O'Young P, Kyaw W, Laletin T, Francis H, Semaan C, Sharifi Tabar M, Singh K, Mullighan C, Wolkenhauer O, Schmitz U and Rasko J (2021) Structure–function relationships explain CTCF zinc finger mutation phenotypes in cancer. Cellular and Molecular Life Sciences, 78. pp. 7519-7536
• Dhungel B, Monteuuis G, Giardina C, Tabar M, Feng Y, Metierre C, Ho S, Nagarajah R, Fontaine A, Shah J, Gokal D, Bailey C, Schmitz U and Rasko J (2021) The fusion of CLEC12A and MIR223HG arises from a trans?splicing event in normal and transformed human cells. International Journal of Molecular Sciences, 22.
• Aghajani M, Yang T, Schmitz U, James A, McCafferty C, de Souza P, Niles N and Roberts T (2020) Epithelial-to-mesenchymal transition and its association with PD-L1 and CD8 in thyroid cancer. Endocrine Connections, 9. pp. 1028-1041

Book Chapters

• Schmitz U (2023) Overview of Computational and Experimental Methods to Identify Tissue-Specific MicroRNA Targets. In: MicroRNA Detection and Target Identification. Methods in Molecular Biology, 2630. Humana Press, New York, NY, USA, pp. 155-177
• Lai X, Schmitz U and Vera J (2022) The Role of MicroRNAs in Cancer Biology and Therapy from a Systems Biology Perspective. In: The Role of MicroRNAs in Cancer Biology and Therapy from a Systems Biology Perspective. Advances in Experimental Medicine and Biology, 1385. Springer, Cham, pp. 1-22
• Schmitz U, Monteuuis G, Petrova V, Shah J and Rasko J (2021) Computational methods for intron retention identification and quantification. In: Systems Medicine: integrative, qualitative and computational approaches. Academic Press, London Wall, United Kingdom, pp. 63-74

More

ResearchOnline@JCU stores 38+ research outputs authored by A/PROF Ulf Schmitz from 2015 onwards.

Current and recent Research Funding to JCU is shown by funding source and project.

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These Higher Degree Research projects are either current or by students who have completed their studies within the past 5 years at JCU. Linked titles show theses available within ResearchOnline@JCU.

Current

• Targeting DNA Repair in HCC through Synthetic Lethality (PhD , Secondary Advisor)
• Immune signatures of inflammatory lung disease (PhD , Secondary Advisor)
• Analysing the role of chimeric transcripts in human cancers (PhD , Primary Advisor/AM/Adv)
• Insights into the molecular bases of coral-specific traits (PhD , Secondary Advisor)
• Pharmacogenomic Profiling of Mental Health Patients in the Philippine National Center for Mental Health (PhD , Secondary Advisor)
• Investigating monocyte and NK derived MS genes by scSequencing, flow cytometry and cytotoxicity assays. (PhD , Secondary Advisor)

The map shows research collaborations by institution from the past 7 years.
Note: Map points are indicative of the countries or states that institutions are associated with.